Nicholas J. Heredia

High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number

Digital PCR enables the absolute quantitation of nucleic acids in a sample. The lack of scalable and practical technologies for digital PCR implementation has hampered the widespread adoption of this inherently powerful technique. Here we describe a high-throughput droplet digital PCR (ddPCR) system that enables processing of ∼2 million PCR reactions using conventional TaqMan assays with a 96-well plate workflow. Three applications demonstrate that the massive partitioning afforded by our ddPCR system provides orders of magnitude more precision and sensitivity than real-time PCR. First, we show the accurate measurement of germline copy number variation. Second, for rare alleles, we show sensitive detection of mutant DNA in a 100 000-fold excess of wildtype background. Third, we demonstrate absolute quantitation of circulating fetal and maternal DNA from cell-free plasma. We anticipate this ddPCR system will allow researchers to explore complex genetic landscapes, discover and validate new disease associations, and define a new era of molecular diagnostics.

Comparison of soft and hard tissue ablation with sub-ps and ns pulse lasers

Tissue ablation with ultrashort laser pulses offers several unique advantages. The nonlinear energy deposition is insensitive to tissue type allowing this tool to be used for soft and hard tissue ablation. The localized energy deposition leads to precise ablation depth and minimal collateral damage. In this paper we will report on our efforts to study and demonstrate tissue ablation using an ultrashort pulse laser. The ablation efficiency, and extent of collateral damage for 0.3 ps and 1000 ps duration laser pulses will be compared. Temperature measurements of the rear surface of a tooth section will also be presented.

Laser tissue welding mediated with a protein solder

A study of laser tissue welding mediated with an indocyanine green dye-enhanced protein solder was performed. Freshly obtained sections of porcine artery were used for the experiments. Sample arterial wall thickness ranged from two to three millimeters. Incisions approximately four millimeters in length were treated using an 805 nanometer continuous- wave diode laser coupled to a one millimeter diameter fiber. Controlled parameters included the power delivered by the laser, the duration of the welding process, and the concentration of dye in the solder. A two-color infrared detection system was constructed to monitor the surface temperatures achieved at the weld site. Burst pressure measurements were made to quantify the strengths of the welds immediately following completion of the welding procedure.

Temperature Feedback and Collagen Cross-Linking in Argon Laser Vascular Welding

Abstract. A preliminary single-animal study of in vivo argon laser vascular welding was conducted using a canine model. The effects of temperature feedback control and saline drip cooling on patency and collagen cross-linking were investigated. The surface temperature at the centre of the laser spot was monitored using a two-colour infrared thermometer. The surface temperature was limited by either a saline drip or feedback control of the laser. Acute patency was evaluated and collagen cross-link assays were performed. Though both protocols yielded successful tissue fusion, welds maintained at a surface temperature of 50°C using feedback control had an elevated cross-link count compared to controls, whereas tissues irradiated without feedback control experienced a cross-link decrease. Simulations using the LATIS (LAser-TISsue) computer code suggest that drip-cooled procedures achieve significantly higher temperatures beneath the tissue surface than temperature feedback-controlled procedures. Differences between the volumetric heating associated with drip-cooled and feedback-controlled protocols may account for the different effects on collagen cross-links. Covalent mechanisms may play a role in argon laser vascular fusion.

In vitro double transposition for DNA identification

We present a double transposition technique that inserts two different transposons into target DNA to act as priming sites for amplifying the region between the two transposons for sequencing applications. Unlike some current sequencing approaches, the genome of the unknown target remains intact in this method. The transposition reaction, DNA repair, and subsequent sequencing were performed entirely in vitro, without the need for transformation into bacteria, and resulted in sequence homology with the plasmid DNA target. This approach can reduce the time required for the assay by more than a day compared with standard techniques and reduces the number of required enzymatic steps. In addition, the in vitro method enables transposition to be carried out in automated microfluidic platforms without the need for significant sample manipulation. As a demonstration of incorporating transposition techniques into high-throughput technologies, single transposition reactions were carried out in picoliter-sized droplets generated on a microfluidic platform.

Experimental and computational laser tissue welding using a protein patch.

An in vitro study of laser tissue welding mediated with a dye-enhanced protein patch was conducted. Fresh sections of porcine aorta were used for the experiments. Arteriotomies were treated using an indocyanine green dye-enhanced collagen patch activated by an 805-nm continuous-wave fiber-delivered diode laser. Temperature histories of the surface of the weld site were obtained using a hollow glass optical fiber-based two-color infrared thermometer. The experimental effort was complemented by simulations with the LATIS (LAser-TISsue) computer code, which uses coupled Monte Carlo, thermal transport, and mass transport models. Comparison of simulated and experimental thermal data indicated that evaporative cooling clamped the surface temperature of the weld site below 100 °C. For fluences of approximately 200 J/cm2, peak surface temperatures averaged 74°C and acute burst strengths consistently exceeded 0.14×106 dyn/cm (hoop tension). The combination of experimental and simulation results showed that the inclusion of water transport and evaporative losses in the computer code has a significant impact on the thermal distributions and hydration levels throughout the tissue volume. The solid-matrix protein patch provided a means of controllable energy delivery and yielded consistently strong welds.

Dynamics of laser-induced transients produced by nanosecond-duration pulses

We have implemented an interferometric method to probe the dynamics of transients induced in absorbing water solutions with nanosecond laser pulses delivered through an optical fiber. We examined two cases corresponding to strong absorption (deposition within 30 micrometers of the fiber tip) and moderate absorption (deposition within 500 micrometers of the fiber tip). With strong absorption the deposited energy leads to a strong stress transient followed by development of a thermally generated vapor bubble. Moderate absorption leads to a moderate stress transient and formation of a cavitation bubble cloud arising from tensile stresses that are produced in the absorbing fluid.

Opto-acoustic cell permeation

Optically generated acoustic waves have been used to temporarily permeate biological cells. This technique may be useful for enhancing transfection of DNA into cells or enhancing the absorption of locally delivered drugs. A diode- pumped frequency-doubled Nd:YAG laser operating a kHz repetition rates was used to produce a series of acoustic pulses. An acoustic wave was formed via thermoelastic expansion by depositing laser radiation into an absorbing dye. Generated pressures were measured with a PVDF hydrophone. The acoustic waves were transmitted to culture and plated cells. The cell media contained a selection of normally-impermeable fluorescent-labeled dextran dyes. Following treatment with the opto-acoustic technique, cellular incorporation of dyes, up to 40,000 Molecular Weight, was noted. Control cells that did not receive opto-acoustic treatment had unremarkable dye incorporation. Uptake of dye was quantified via fluorescent microscopic analysis. Trypan Blue membrane exclusion assays and fluorescent labeling assays confirmed the vitality of cells following treatment. This method of enhanced drug delivery has the potential to dramatically reduce required drug dosages and associated side effects and enable revolutionary therapies.

In vivo argon laser vascular welding using thermal feedback: open- and closed-loop patency and collagen crosslinking

An in vivo study of vascular welding with a fiber-delivered argon laser was conducted using a canine model. Longitudinal arteriotomies and venotomies were treated on femoral vein and artery. Laser energy was delivered to the vessel wall via a 400 micrometer optical fiber. The surface temperature at the center of the laser spot was monitored in real time using a hollow glass optical fiber-based two-color infrared thermometer. The surface temperature was limited by either a room-temperature saline drip or direct feedback control of the laser using a mechanical shutter to alternately pass and block the laser. Acute patency was evaluated either visually (leak/no leak) or by in vivo burst pressure measurements. Biochemical assays were performed to investigate the possible laser-induced formation or destruction of enzymatically mediated covalent crosslinks between collagen molecules. Viable welds were created both with and without the use of feedback control. Tissues maintained at 50 degrees Celsius using feedback control had an elevated crosslink count compared to controls, while those irradiated without feedback control experienced a decrease. Differences between the volumetric heating associated with open and closed loop protocols may account for the different effects on collagen crosslinks. Covalent mechanisms may play a role in argon laser vascular fusion.

Laser welding and collagen crosslinks

The strength and stability of laser-welded tissue may be influenced, in part, by the effects of laser exposure on collagen crosslinking. We therefore studied the effects of diode laser exposure (805 nm, 1 - 8 watts, 30 seconds) plus indocyanine green dye (ICG) on calf tail tendon collagen crosslinks. The effect of ICG dye alone on crosslink content prior to laser exposure was investigated; unexpectedly, we found that ICG-treated tissue had significantly increased DHLNL and OHP, but not HLNL. Laser exposure after ICG application reduced elevated DHLNL and OHP crosslink content down to their native levels. The monohydroxylated crosslink HLNL was inversely correlated with laser output (p less than 0.01 by linear regression analysis). DHLNL content was highly correlated with content of its maturational product, OHP, suggesting that precursor-product relationships are maintained. We conclude that: (1) ICG alone induces DHLNL and OHP crosslink formation; (2) subsequent laser exposure reduces the ICG-induced crosslinks down to native levels; (3) excessive diode laser exposure destroys normally occurring HLNL crosslinks.